A man believed to be Mullah Abdul Ghani Baradar in a photograph taken in 1998, given to The New York Times by a former photographer for the Taliban.

WASHINGTON — The Taliban’s top military commander was captured several days ago in Karachi, Pakistan, in a secret joint operation by Pakistani and American intelligence forces, according to American government officials.

The commander, Mullah Abdul Ghani Baradar, is an Afghan described by American officials as the most significant Taliban figure to be detained since the American-led war in Afghanistan started more than eight years ago. He ranks second in influence only to Mullah Muhammad Omar, the Taliban’s founder and a close associate of Osama bin Laden before the Sept. 11 attacks.

Mullah Baradar has been in Pakistani custody for several days, with American and Pakistani intelligence officials both taking part in interrogations, according to the officials.

It was unclear whether he was talking, but the officials said his capture had provided a window into the Taliban and could lead to other senior officials. Most immediately, they hope he will provide the whereabouts of Mullah Omar, the one-eyed cleric who is the group’s spiritual leader.

His capture could cripple the Taliban’s military operations, at least in the short term, said Bruce O. Riedel, a former C.I.A. officer who last spring led the Obama administration’s Afghanistan and Pakistan policy review.

Details of the raid remain murky, but officials said that it had been carried out by Pakistan’s military spy agency, the Directorate for Inter-Services Intelligence, or ISI, and that C.I.A. operatives had accompanied the Pakistanis.

The New York Times learned of the operation on Thursday, but delayed reporting it at the request of White House officials, who contended that making it public would end a hugely successful intelligence-gathering effort. The officials said that the group’s leaders had been unaware of Mullah Baradar’s capture and that if it became public they might cover their tracks and become more careful about communicating with each other.

The Times is publishing the news now because White House officials acknowledged that the capture of Mullah Baradar was becoming widely known in the region.

Several American government officials gave details about the raid on the condition that they not be named, because the operation was classified.

American officials believe that besides running the Taliban’s military operations, Mullah Baradar runs the group’s leadership council, often called the Quetta Shura because its leaders for years have been thought to be hiding near Quetta, the capital of Baluchistan Province in Pakistan.

A spokesman for the Taliban insisted on Tuesday that Baradar was still free.

“This is just rumor spread by foreigners to divert attention from the Marja offensive,” said the spokesman, Zabiullah Mujahid.

“They are facing big problems in Marja. In reality there is nothing regarding Baradar’s arrest. He is safe and free and he is in Afghanistan.”

The participation of Pakistan’s spy service could suggest a new level of cooperation from Pakistan’s leaders, who have been ambivalent about American efforts to crush the Taliban. Increasingly, the Americans say, senior leaders in Pakistan, including the chief of its army, Gen. Ashfaq Parvez Kayani, have gradually come around to the view that they can no longer support the Taliban in Afghanistan — as they have quietly done for years — without endangering themselves. Indeed, American officials have speculated that Pakistani security officials could have picked up Mullah Baradar long ago.

The officials said that Pakistan was leading the interrogation of Mullah Baradar, but that Americans were also involved. The conditions of the questioning are unclear. In its first week in office, the Obama administration banned harsh interrogations like waterboarding by Americans, but the Pakistanis have long been known to subject prisoners to brutal questioning.

American intelligence officials believe that elements within Pakistan’s security services have covertly supported the Taliban with money and logistical help — largely out of a desire to retain some ally inside Afghanistan for the inevitable day when the Americans leave.

The ability of the Taliban’s top leaders to operate relatively freely inside Pakistan has for years been a source of friction between the ISI and the C.I.A. Americans have complained that they have given ISI operatives the precise locations of Taliban leaders, but that the Pakistanis usually refuse to act.

The Pakistanis have countered that the American intelligence was often outdated, or that faulty information had been fed to the United States by Afghanistan’s intelligence service.

For the moment it is unclear how the capture of Mullah Baradar will affect the overall direction of the Taliban, who have so far refused to disavow Al Qaeda and to accept the Afghan Constitution. American officials have hoped to win over some midlevel members of the group.

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Mr. Riedel, the former C.I.A. official, said that he had not heard about Mullah Baradar’s capture before being contacted by The Times, but that the raid constituted a “sea change in Pakistani behavior.”

In recent weeks, American officials have said they have seen indications that the Pakistani military and spy services may finally have begun to distance themselves from the Taliban. One Obama administration official said Monday that the White House had “no reason to think that anybody was double-dealing at all” in aiding in the capture of Mullah Baradar.

A parade of American officials traveling to the Pakistani capital have made the case that the Afghan Taliban are now aligned with groups — like the Pakistani Taliban — that threaten the stability of the Pakistani government.

Mullah Baradar oversees the group’s operations across its primary area of activity in southern and western Afghanistan. While some of the insurgent groups active in Afghanistan receive only general guidance from their leaders, the Taliban are believed to be somewhat hierarchical, with lower-ranking field commanders often taking directions and orders from their leaders across the border.

In an attempt to improve the Taliban’s image both inside the country and abroad, Mullah Baradar last year helped issue a “code of conduct” for Taliban fighters. The handbook, small enough to be carried in the pocket of each Taliban foot soldier, gave specific guidance about topics including how to avoid civilian casualties, how to win the hearts and minds of villagers, and the necessity of limiting suicide attacks to avoid a backlash.

In recent months, a growing number of Taliban leaders are believed to have fled to Karachi, a sprawling, chaotic city in southern Pakistan hundreds of miles from the turbulence of the Afghan frontier. A diplomat based in Kabul, speaking on the condition of anonymity, said in an interview last month that Mullah Omar had moved to Karachi, and that several of his colleagues were there, too.

The leadership council, which includes more than a dozen of the Taliban’s best-known leaders, charts the overall direction of the war, assigns Taliban “shadow governors” to run many Afghan provinces and districts, and chooses battlefield commanders. It also oversees a number of subcommittees that direct other aspects of the war, like political, religious and military affairs.

According to Wahid Muzhda, a former Taliban official in Kabul who stays in touch with former colleagues, the council meets every three or four months to plot strategy. As recently as three years ago, he said, the council had 19 members. Since then, six have been killed or captured. Others have since filled the empty seats, he said.

Among the council members killed were Mullah Dadullah, who died during a raid by NATO and Afghan forces in 2007. Among the captured were Mullah Obaidullah, the Taliban defense minister, who reported to Mr. Baradar.

“The only man more powerful than Baradar is Omar,” Mr. Muzhda said. “He and Omar cannot meet very often because of security reasons, but they have a very good relationship.”

Western and Afghan officials familiar with the workings of the Taliban’s leadership have described Mullah Baradar as one of the Taliban’s most approachable leaders, and the one most ready to negotiate with the Afghan government.

Mediators who have worked to resolve kidnappings and other serious issues have often approached the Taliban leadership through him.

As in the case of the reclusive Mullah Omar, the public details of Mullah Baradar’s life are murky. According to an Interpol alert, he was born in 1968 in Weetmak, a village in Afghanistan’s Oruzgan Province. Terrorism experts describe him as a skilled military leader who runs many high-level meetings of the Taliban’s top commanders in Afghanistan.

In answers to questions submitted by Newsweek last summer, Mullah Baradar said that he could not maintain “continuous contacts” with Mullah Omar, but that he received advice on “important topics” from the cleric.

In the same interview, Mullah Baradar said he welcomed a large increase in American troops in Afghanistan because the Taliban “want to inflict maximum losses on the Americans, which is possible only when the Americans are present here in large numbers and come out of their fortified places.”

Shortly after the Sept. 11 attacks, Mullah Baradar was assigned by Mullah Omar to assume overall command of Taliban forces in northern Afghanistan. In that role, he oversaw a large group of battle-hardened Arab and foreign fighters who were based in the northern cities of Kunduz and Mazar-i-Sharif.

In November 2001, as Taliban forces collapsed after the American invasion, Mullah Baradar and several other senior Taliban leaders were captured by Afghan militia fighters aligned with the United States. But Pakistani intelligence operatives intervened, and Mullah Baradar and the other Taliban leaders were released, according to a senior official of the Northern Alliance, the group of Afghans aligned with the United States.

A version of this article appears in print on February 16, 2010, on Page A1 of the New York edition with the headline: Secret Joint Raid Captures Taliban’s Top Commander. Order Reprints|Today's Paper|Subscribe